I think the two FreeTexts in your video fails to delete because the position is jumping as you are entering the value:
For example, the B text, notice the shift between adding the FreeText.
This is likely causing this line to not work: Annot selectedAnnotation = page.getAnnot(pos);
This appears to be related to your custom implementation as the soft keyboard should not be pushing the FreeText box around you can verify the behaviour on our Showcase demo app
The issue is that the index is not a good way to retrieve your annotation, as it can change when you make modifications to the document (such as adding or removing annotations).
We recommend for you to instead store the ID for the annotation to ensure the lookup is correct, for example: Annot.getUniqueID().getAsPDFText()
To retrieve via this ID you can call: ViewerUtils.getAnnotById(PDFDoc doc, String id, int page num)
And then to properly delete this annot call: AnnotUtils.safeDeleteAnnotAndUpdate(PDFViewCtrl pdfViewCtrl, Annot annot, int pageNum)
Please give this a try and see if it resolves your issue.